Publications
| 2022 |
|---|
| Shen, S. S.; Nanda, H.; Aliferis, C.; Langlois, R. A. Characterization of Influenza A Virus Induced Transposons Reveals a Subgroup of Transposons Likely Possessing the Regulatory Role as ERNAs. Sci Rep 2022, 12 (1), 2188. https://doi.org/10.1038/s41598-022-06196-6. |
| Huang, Z.; Zhang, Z.; Moazzami, Z.; Heck, R.; Hu, P.; Nanda, H.; Ren, K.; Sun, Z.; Bartolomucci, A.; Gao, Y.; Chung, D.; Zhu, W.; Shen, S.; Ruan, H.-B. Brown Adipose Tissue Involution Associated with Progressive Restriction in Progenitor Competence. Cell Reports 2022, 39 (2). https://doi.org/10.1016/j.celrep.2022.110575. |
| Burrack, A. L.; Spartz, E. J.; Rollins, M. R.; Miller, E. A.; Firulyova, M.; Cruz, E.; Goldberg, M. F.; Wang, I. X.; Nanda, H.; Shen, S.; Zaitsev, K.; Stromnes, I. M. Cxcr3 Constrains Pancreatic Cancer Dissemination through Instructing T Cell Fate. Cancer Immunol Immunother 2022. https://doi.org/10.1007/s00262-022-03338-7. |
| 2021 |
| Zakharia, Y.; McWilliams, R. R.; Rixe, O.; Drabick, J.; Shaheen, M. F.; Grossmann, K. F.; Kolhe, R.; Pacholczyk, R.; Sadek, R.; Tennant, L. L.; Smith, C. M.; Kennedy, E. P.; Jr, C. J. L.; Vahanian, N. N.; Yu, J.; Shen, S. S.; Brincks, E. L.; Rossi, G. R.; Munn, D.; Milhem, M. Phase II Trial of the IDO Pathway Inhibitor Indoximod plus Pembrolizumab for the Treatment of Patients with Advanced Melanoma. J Immunother Cancer 2021, 9 (6), e002057. https://doi.org/10.1136/jitc-2020-002057. |
| Qiu, X.; Macchietto, M. G.; Liu, X.; Lu, Y.; Ma, Y.; Guo, H.; Saqui-Salces, M.; Bernlohr, D. A.; Chen, C.; Shen, S.; Chen, X. Identification of Gut Microbiota and Microbial Metabolites Regulated by an Antimicrobial Peptide Lipocalin 2 in High Fat Diet-Induced Obesity. Int J Obes 2021, 45 (1), 143–154. https://doi.org/10.1038/s41366-020-00712-2. |
| Fiege, J. K.; Thiede, J. M.; Nanda, H. A.; Matchett, W. E.; Moore, P. J.; Montanari, N. R.; Thielen, B. K.; Daniel, J.; Stanley, E.; Hunter, R. C.; Menachery, V. D.; Shen, S. S.; Bold, T. D.; Langlois, R. A. Single Cell Resolution of SARS-CoV-2 Tropism, Antiviral Responses, and Susceptibility to Therapies in Primary Human Airway Epithelium. PLOS Pathogens 2021, 17 (1), e1009292. https://doi.org/10.1371/journal.ppat.1009292. |
| Fiege, J. K.; Block, K. E.; Pierson, M. J.; Nanda, H.; Shepherd, F. K.; Mickelson, C. K.; Stolley, J. M.; Matchett, W. E.; Wijeyesinghe, S.; Meyerholz, D. K.; Vezys, V.; Shen, S. S.; Hamilton, S. E.; Masopust, D.; Langlois, R. A. Mice with Diverse Microbial Exposure Histories as a Model for Preclinical Vaccine Testing. Cell Host Microbe 2021, 29 (12), 1815-1827.e6. https://doi.org/10.1016/j.chom.2021.10.001. |
| 2020 |
| Macchietto, M. G.; Langlois, R. A.; Shen, S. S. Virus-Induced Transposable Element Expression up-Regulation in Human and Mouse Host Cells. Life Sci Alliance 2020, 3 (2), e201900536. https://doi.org/10.26508/lsa.201900536. |
| Fay, E. J.; Aron, S. L.; Macchietto, M. G.; Markman, M. W.; Esser-Nobis, K.; Jr, M. G.; Shen, S.; Langlois, R. A. Cell Type- and Replication Stage-Specific Influenza Virus Responses in Vivo. PLOS Pathogens 2020, 16 (8), e1008760. https://doi.org/10.1371/journal.ppat.1008760. |
| Chen, Q. Y.; Shen, S.; Sun, H.; Wu, F.; Kluz, T.; Kibriya, M. G.; Chen, Y.; Ahsan, H.; Costa, M. PBMC Gene Expression Profiles of Female Bangladeshi Adults Chronically Exposed to Arsenic-Contaminated Drinking Water. Environmental Pollution 2020, 259, 113672. https://doi.org/10.1016/j.envpol.2019.113672. |
| Chen, D.; Chen, Q. Y.; Wang, Z.; Zhu, Y.; Kluz, T.; Tan, W.; Li, J.; Wu, F.; Fang, L.; Zhang, X.; He, R.; Shen, S.; Sun, H.; Zang, C.; Jin, C.; Costa, M. Polyadenylation of Histone H3.1 MRNA Promotes Cell Transformation by Displacing H3.3 from Gene Regulatory Elements. iScience 2020, 23 (9). https://doi.org/10.1016/j.isci.2020.101518. |
| 2019 |
| Fiege, J. K.; Stone, I. A.; Fay, E. J.; Markman, M. W.; Wijeyesinghe, S.; Macchietto, M. G.; Shen, S.; Masopust, D.; Langlois, R. A. The Impact of TCR Signal Strength on Resident Memory T Cell Formation during Influenza Virus Infection. The Journal of Immunology 2019, 203 (4), 936–945. https://doi.org/10.4049/jimmunol.1900093. |
| 2018 |
| Xiong, X.; Schober, M.; Tassone, E.; Khodadadi-Jamayran, A.; Sastre-Perona, A.; Zhou, H.; Tsirigos, A.; Shen, S.; Chang, M.; Melamed, J.; Ossowski, L.; Wilson, E. L. KLF4, A Gene Regulating Prostate Stem Cell Homeostasis, Is a Barrier to Malignant Progression and Predictor of Good Prognosis in Prostate Cancer. Cell Reports 2018, 25 (11), 3006-3020.e7. https://doi.org/10.1016/j.celrep.2018.11.065. |
| Winterhoff, B.; Kommoss, S.; Heitz, F.; Konecny, G. E.; Dowdy, S. C.; Mullany, S. A.; Park-Simon, T.-W.; Baumann, K.; Hilpert, F.; Brucker, S.; du Bois, A.; Schröder, W.; Burges, A.; Shen, S.; Wang, J.; Tourani, R.; Ma, S.; Pfisterer, J.; Aliferis, C. F. Developing a Clinico-Molecular Test for Individualized Treatment of Ovarian Cancer: The Interplay of Precision Medicine Informatics with Clinical and Health Economics Dimensions. AMIA Annu Symp Proc 2018, 2018, 1093–1102. |
| Sjaastad, L. E.; Fay, E. J.; Fiege, J. K.; Macchietto, M. G.; Stone, I. A.; Markman, M. W.; Shen, S.; Langlois, R. A. Distinct Antiviral Signatures Revealed by the Magnitude and Round of Influenza Virus Replication in Vivo. Proceedings of the National Academy of Sciences 2018, 115 (38), 9610–9615. https://doi.org/10.1073/pnas.1807516115. |
| Beura, L. K.; Wijeyesinghe, S.; Thompson, E. A.; Macchietto, M. G.; Rosato, P. C.; Pierson, M. J.; Schenkel, J. M.; Mitchell, J. S.; Vezys, V.; Fife, B. T.; Shen, S.; Masopust, D. T Cells in Nonlymphoid Tissues Give Rise to Lymph-Node-Resident Memory T Cells. Immunity 2018, 48 (2), 327-338.e5. https://doi.org/10.1016/j.immuni.2018.01.015. |
| 2017 |
| Gao, J.-L.; Wei, M.-F.; Zhou, X.-Y.; Ke, K.-F.; Sang, A.-M.; Guan, Y.-F.; Cheng, C.; Steven, S. S. Perspectives on Personalized Precision Medicine: Problems and Challenges in Research and Clinical Practice. Progress in Physiological Sciences 2017, 48 (4), 241–248. |
| 2016 |
| Yao, Y.; Chen, T.; Shen, S. S.; Niu, Y.; DesMarais, T. L.; Linn, R.; Saunders, E.; Fan, Z.; Lioy, P.; Kluz, T.; Chen, L.-C.; Wu, Z.; Costa, M. Corrigendum to “Malignant Human Cell Transformation of Marcellus Shale Gas Drilling Flow Back Water” [Toxicol. Appl. Pharmacol. (288/1) (2015) 121–130]. Toxicology and Applied Pharmacology 2016, 296, 85. https://doi.org/10.1016/j.taap.2016.02.006. |
| Yang, Y.; Li, W.; Hoque, M.; Hou, L.; Shen, S.; Tian, B.; Dynlacht, B. D. PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation. PLOS Genetics 2016, 12 (1), e1005794. https://doi.org/10.1371/journal.pgen.1005794. |
| Yang, Y.; Li, W.; Hoque, M.; Hou, L.; Shen, S.; Tian, B.; Dynlacht, B. D. Correction: PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation. PLOS Genetics 2016, 12 (2), e1005883. https://doi.org/10.1371/journal.pgen.1005883. |
| Wu, F.; Jordan, A.; Kluz, T.; Shen, S.; Sun, H.; Cartularo, L. A.; Costa, M. SATB2 Expression Increased Anchorage-Independent Growth and Cell Migration in Human Bronchial Epithelial Cells. Toxicology and Applied Pharmacology 2016, 293, 30–36. https://doi.org/10.1016/j.taap.2016.01.008. |
| Lauterstein, D. E.; Tijerina, P. B.; Corbett, K.; Akgol Oksuz, B.; Shen, S. S.; Gordon, T.; Klein, C. B.; Zelikoff, J. T. Frontal Cortex Transcriptome Analysis of Mice Exposed to Electronic Cigarettes During Early Life Stages. International Journal of Environmental Research and Public Health 2016, 13 (4), 417. https://doi.org/10.3390/ijerph13040417. |
| Cartularo, L.; Kluz, T.; Cohen, L.; Shen, S. S.; Costa, M. Molecular Mechanisms of Malignant Transformation by Low Dose Cadmium in Normal Human Bronchial Epithelial Cells. PLOS ONE 2016, 11 (5), e0155002. https://doi.org/10.1371/journal.pone.0155002. |
| 2015 |
| Yao, Y.; Chen, T.; Shen, S. S.; Niu, Y.; DesMarais, T. L.; Linn, R.; Saunders, E.; Fan, Z.; Lioy, P.; Kluz, T.; Chen, L.-C.; Wu, Z.; Costa, M. Malignant Human Cell Transformation of Marcellus Shale Gas Drilling Flow Back Water. Toxicology and Applied Pharmacology 2015, 288 (1), 121–130. https://doi.org/10.1016/j.taap.2015.07.011. |
| Wilson, A. A.; Ying, L.; Liesa, M.; Segeritz, C.-P.; Mills, J. A.; Shen, S. S.; Jean, J.; Lonza, G. C.; Liberti, D. C.; Lang, A. H.; Nazaire, J.; Gower, A. C.; Müeller, F.-J.; Mehta, P.; Ordóñez, A.; Lomas, D. A.; Vallier, L.; Murphy, G. J.; Mostoslavsky, G.; Spira, A.; Shirihai, O. S.; Ramirez, M. I.; Gadue, P.; Kotton, D. N. Emergence of a Stage-Dependent Human Liver Disease Signature with Directed Differentiation of Alpha-1 Antitrypsin-Deficient IPS Cells. Stem Cell Reports 2015, 4 (5), 873–885. https://doi.org/10.1016/j.stemcr.2015.02.021. |
| Shaik-Dasthagirisaheb, Y. B.; Huang, N.; Weinberg, E. O.; Shen, S. S.; Genco, C. A.; Gibson III, F. C. Aging and Contribution of MyD88 and TRIF to Expression of TLR Pathway-Associated Genes Following Stimulation with Porphyromonas Gingivalis. Journal of Periodontal Research 2015, 50 (1), 89–102. https://doi.org/10.1111/jre.12185. |
| Montenegro, D.; Kalpana, K.; Chrissian, C.; Sharma, A.; Takaoka, A.; Iacovidou, M.; Soll, C. E.; Aminova, O.; Heguy, A.; Cohen, L.; Shen, S.; Kawamura, A. Uncovering Potential ‘Herbal Probiotics’ in Juzen-Taiho-to through the Study of Associated Bacterial Populations. Bioorganic & Medicinal Chemistry Letters 2015, 25 (3), 466–469. https://doi.org/10.1016/j.bmcl.2014.12.036. |
| Maass, K.; Shekhar, A.; Lu, J.; Kang, G.; See, F.; Kim, E. E.; Delgado, C.; Shen, S.; Cohen, L.; Fishman, G. I. Isolation and Characterization of Embryonic Stem Cell-Derived Cardiac Purkinje Cells. Stem Cells 2015, 33 (4), 1102–1112. https://doi.org/10.1002/stem.1921. |
| Laulicht, F.; Brocato, J.; Cartularo, L.; Vaughan, J.; Wu, F.; Kluz, T.; Sun, H.; Oksuz, B. A.; Shen, S.; Peana, M.; Medici, S.; Zoroddu, M. A.; Costa, M. Tungsten-Induced Carcinogenesis in Human Bronchial Epithelial Cells. Toxicology and Applied Pharmacology 2015, 288 (1), 33–39. https://doi.org/10.1016/j.taap.2015.07.003. |
| Cimmino, L.; Dawlaty, M. M.; Ndiaye-Lobry, D.; Yap, Y. S.; Bakogianni, S.; Yu, Y.; Bhattacharyya, S.; Shaknovich, R.; Geng, H.; Lobry, C.; Mullenders, J.; King, B.; Trimarchi, T.; Aranda-Orgilles, B.; Liu, C.; Shen, S.; Verma, A. K.; Jaenisch, R.; Aifantis, I. TET1 Is a Tumor Suppressor of Hematopoietic Malignancy. Nat Immunol 2015, 16 (6), 653–662. https://doi.org/10.1038/ni.3148. |
| Cimmino, L.; Dawlaty, M. M.; Ndiaye-Lobry, D.; Yap, Y. S.; Bakogianni, S.; Yu, Y.; Bhattacharyya, S.; Shaknovich, R.; Geng, H.; Lobry, C.; Mullenders, J.; King, B.; Trimarchi, T.; Aranda-Orgilles, B.; Liu, C.; Shen, S.; Verma, A. K.; Jaenisch, R.; Aifantis, I. Erratum: TET1 Is a Tumor Suppressor of Hematopoietic Malignancy. Nat Immunol 2015, 16 (8), 889–889. https://doi.org/10.1038/ni0815-889a. |
| Chatterjee, S. S.; Saj, A.; Gocha, T.; Murphy, M.; Gonsalves, F. C.; Zhang, X.; Hayward, P.; Akgöl Oksuz, B.; Shen, S. S.; Madar, A.; Martinez Arias, A.; DasGupta, R. Inhibition of β-Catenin–TCF1 Interaction Delays Differentiation of Mouse Embryonic Stem Cells. Journal of Cell Biology 2015, 211 (1), 39–51. https://doi.org/10.1083/jcb.201503017. |
| 2014 |
| Tee, W.-W.; Shen, S. S.; Oksuz, O.; Narendra, V.; Reinberg, D. Erk1/2 Activity Promotes Chromatin Features and RNAPII Phosphorylation at Developmental Promoters in Mouse ESCs. Cell 2014, 156 (4), 678–690. https://doi.org/10.1016/j.cell.2014.01.009. |
| Kaneko, S.; Son, J.; Bonasio, R.; Shen, S. S.; Reinberg, D. Nascent RNA Interaction Keeps PRC2 Activity Poised and in Check. Genes Dev. 2014, 28 (18), 1983–1988. https://doi.org/10.1101/gad.247940.114. |
| Cheng, J.; Blum, R.; Bowman, C.; Hu, D.; Shilatifard, A.; Shen, S.; Dynlacht, B. D. A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers. Molecular Cell 2014, 53 (6), 979–992. https://doi.org/10.1016/j.molcel.2014.02.032. |
| 2013 & older |
| Son, J.; Shen, S. S.; Margueron, R.; Reinberg, D. Nucleosome-Binding Activities within JARID2 and EZH1 Regulate the Function of PRC2 on Chromatin. Genes Dev. 2013, 27 (24), 2663–2677. https://doi.org/10.1101/gad.225888.113. |
| Mills, J. A.; Wang, K.; Paluru, P.; Ying, L.; Lu, L.; Galvão, A. M.; Xu, D.; Yao, Y.; Sullivan, S. K.; Sullivan, L. M.; Mac, H.; Omari, A.; Jean, J.-C.; Shen, S.; Gower, A.; Spira, A.; Mostoslavsky, G.; Kotton, D. N.; French, D. L.; Weiss, M. J.; Gadue, P. Clonal Genetic and Hematopoietic Heterogeneity among Human-Induced Pluripotent Stem Cell Lines. Blood 2013, 122 (12), 2047–2051. https://doi.org/10.1182/blood-2013-02-484444. |
| King, B.; Trimarchi, T.; Reavie, L.; Xu, L.; Mullenders, J.; Ntziachristos, P.; Aranda-Orgilles, B.; Perez-Garcia, A.; Shi, J.; Vakoc, C.; Sandy, P.; Shen, S. S.; Ferrando, A.; Aifantis, I. XThe Ubiquitin Ligase FBXW7 Modulates Leukemia-Initiating Cell Activity by Regulating MYC Stability. Cell 2013, 153 (7), 1552. https://doi.org/10.1016/j.cell.2013.05.041. |
| Kaneko, S.; Son, J.; Shen, S. S.; Reinberg, D.; Bonasio, R. PRC2 Binds Active Promoters and Contacts Nascent RNAs in Embryonic Stem Cells. Nature Structural Biology 2013, 20 (11), 1258–1264. https://doi.org/10.1038/nsmb.2700. |
| Tagne, J. B.; Gupta, S.; Gower, A. C.; Shen, S. S.; Varma, S.; Lakshminarayanan, M.; Cao, Y.; Spira, A.; Volkert, T. L.; Ramirez, M. I. Genome-Wide Analyses of Nkx2-1 Binding to Transcriptional Target Genes Uncover Novel Regulatory Patterns Conserved in Lung Development and Tumors. PLoS One 2012, 7 (1). https://doi.org/10.1371/journal.pone.0029907. |
| Sommer, C. A.; Christodoulou, C.; Gianotti-Sommer, A.; Shen, S. S.; Sailaja, B. S.; Hezroni, H.; Spira, A.; Meshorer, E.; Kotton, D. N.; Mostoslavsky, G. Residual Expression of Reprogramming Factors Affects the Transcriptional Program and Epigenetic Signatures of Induced Pluripotent Stem Cells. PLoS One 2012, 7 (12). https://doi.org/10.1371/journal.pone.0051711. |
| Longmire, T. A.; Ikonomou, L.; Hawkins, F.; Christodoulou, C.; Cao, Y.; Jean, J. C.; Kwok, L. W.; Mou, H.; Rajagopal, J.; Shen, S. S.; Dowton, A. A.; Serra, M.; Weiss, D. J.; Green, M. D.; Snoeck, H. W.; Ramirez, M. I.; Kotton, D. N. Efficient Derivation of Purified Lung and Thyroid Progenitors from Embryonic Stem Cells. Cell Stem Cell 2012, 10 (4), 398–411. https://doi.org/10.1016/j.stem.2012.01.019. |
| Cheng, X.; Ying, L.; Lu, L.; Galvão, A. M.; Mills, J. A.; Lin, H. C.; Kotton, D. N.; Shen, S. S.; Nostro, M. C.; Choi, J. K.; Weiss, M. J.; French, D. L.; Gadue, P. Self-Renewing Endodermal Progenitor Lines Generated from Human Pluripotent Stem Cells. Cell Stem Cell 2012, 10 (4), 371–384. https://doi.org/10.1016/j.stem.2012.02.024. |
| Bonasio, R.; Li, Q.; Lian, J.; Mutti, N. S.; Jin, L.; Zhao, H.; Zhang, P.; Wen, P.; Xiang, H.; Ding, Y.; Jin, Z.; Shen, S. S.; Wang, Z.; Wang, W.; Wang, J.; Berger, S. L.; Liebig, J.; Zhang, G.; Reinberg, D. Genome-Wide and Caste-Specific DNA Methylomes of the Ants Camponotus Floridanus and Harpegnathos Saltator. Current Biology 2012, 22 (19), 1755–1764. https://doi.org/10.1016/j.cub.2012.07.042. |
| Beck, D. B.; Oda, H.; Shen, S. S.; Reinberg, D. PR-Set7 and H4K20me1: At the Crossroads of Genome Integrity, Cell Cycle, Chromosome Condensation, and Transcription. Genes and Development 2012, 26 (4), 325–337. https://doi.org/10.1101/gad.177444.111. |
| Christodoulou, C.; Longmire, T. A.; Shen, S. S.; Bourdon, A.; Sommer, C. A.; Gadue, P.; Spira, A.; Gouon-Evans, V.; Murphy, G. J.; Mostoslavsky, G.; Kotton, D. N. Mouse ES and IPS Cells Can Form Similar Definitive Endoderm despite Differences in Imprinted Genes. Journal of Clinical Investigation 2011, 121 (6), 2313–2325. https://doi.org/10.1172/JCI43853. |
| Brooks, W. W.; Shen, S. S.; Conrad, C. H.; Goldstein, R. H.; Bing, O. H. L. Transition from Compensated Hypertrophy to Systolic Heart Failure in the Spontaneously Hypertensive Rat: Structure, Function, and Transcript Analysis. Genomics 2010, 95 (2), 84–92. https://doi.org/10.1016/j.ygeno.2009.12.002. |
| Brooks, W. W.; Shen, S.; Conrad, C. H.; Goldstein, R. H.; Deng, L. L.; Bing, O. H. L. Transcriptional Changes Associated with Recovery from Heart Failure in the SHR. Journal of Molecular and Cellular Cardiology 2010, 49 (3), 390–401. https://doi.org/10.1016/j.yjmcc.2010.06.002. |
| Xu, L.; Shen, S. S.; Hoshida, Y.; Subramanian, A.; Ross, K.; Brunet, J. P.; Wagner, S. N.; Ramaswamy, S.; Mesirov, J. P.; Hynes, R. O. Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases. Cell Growth and Differentiation 2008, 6 (5), 760–769. https://doi.org/10.1158/1541-7786.MCR-07-0344. |
| Wong, S. Y.; Haack, H.; Kissil, J. L.; Barry, M.; Bronson, R. T.; Shen, S. S.; Whittaker, C. A.; Crowley, D.; Hynes, R. O. Protein 4.1B Suppresses Prostate Cancer Progression and Metastasis. Proceedings of the National Academy of Sciences of the United States of America 2007, 104 (31), 12784–12789. https://doi.org/10.1073/pnas.0705499104. |
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